.fastq files obtained by RNA-Seq and I'm trying to map them into customly merged and generated miRNA reference which is taken from miRBase.
I am taking these error.
Could not locate a Bowtie index corresponding to basename "db" Error: Encountered internal Bowtie 2 exception (#1) Command: /usr/bin/bowtie2-align-s --wrapper basic-0 -q -x db --passthrough -U /home/graug/Desktop/mirna/2_R.mirna.cleaned.fastq (ERR): bowtie2-align exited with value 1
To generate index files, I've typed the following code.
bowtie-build mirna_db.fa db
To map RNA-Seq
.fastq files into custom miRNA database of mine, following code was used.
bowtie2 -x db -U -q /mirna/2_R.mirna.cleaned.fastq -S /mirna/2_R.mirna.sam --no-unal
I've checked the db index with
bowtie-inspect command and index seems pretty sanity. Couldn't figure out what am I missing ? Can you help me to find it, please.